Ribonuclease



Ribonuclease (RNase) degrades RNA. The endonucleases cleave single or double stranded RNA and include RNase III, A, T1 H and P. Exo-RNases remove terminal nucleotide from the ends of the RNA molecule. They include RNase II D, T, PH, Polynucleotide Phosphorylase (PNPase) and oligoribonuclease (ORNase). RNase A cleaves C or U of single-stranded RNA (ssRNA). RNase BA is RNase from Bacillus amyloliquefaciens. RNase D degrades 3'-end pre-tRNA. RNase H cleaves RNA/DNA double-strand to produce ssDNA. RNase I cleaves 3'-end of ssRNA. RNase II degrades 3'-end ssRNA. RNase III cleaves rRNA. RNase P is a ribozyme. RNase S is RNase A cleaved by subtilisin. RNase SA is RNase from Streptomyces auerofaciens. RNase T is involved in RNA maturation. RNase T1 cleaves 3'-end G from ssRNA. RNase U2 cleaves 3'-end A from ssRNA.

3D Structures of Ribonuclease
Update June 2011

RNase I
3mwq, 3mwq, 3mx8, 3i67, 3i6f, 3i6h, 3i6j, 3i7w, 3eux, 3euy, 3euz, 3ev0, 3ev1, 3ev2, 3ev3, 3ev4, 3ev5, 3ev6, 3dh5, 2e3w, 2g4w, 2g4x, 2gbq, 2blp, 2blz, 1jvt, 1jvv, 1js0, 1fs3, 1kf2, 1kf3, 1kf4, 1kf5, 1kf7, 1kf8, 1aqp, 1a2w, 1rnw, 1rnz, 1rno, 1rnq, 1rbx, 1ssc, 3srn, 4srn, 1srn, 5rsa, 1afu, 1bel, 1c0b, 1c0c, 1lsq, 1rat, 1rbn, 1rha, 1rhb, 1rnx, 1rny, 1rsm, 1xps, 1xpt, 2g8q, 2rat, 3mzq, 3mzr, 3rat, 3rn3, 4rat, 5rat, 6rat, 7rat, 7rsa, 8rat, 8rsa, 9rat, 9rsa- bRNase I pancreatic - bovine

3a1r - bRNase I pancreatic - neutron

3i7x, 3i7y, 3fkz, 3fl3, 3dh6, 3di7, 3di8, 3di9, 3dib, 3dic, 2oqf, 3bcm, 3bco, 3bcp, 2nui, 2op2, 1ymn, 1ymr, 1ymw, 2apq, 1izp, 1izq, 1izr, 1kh8, 1c8w, 1eic, 1eid, 1eie, 1dy5, 3rsd, 3rsk, 1ssa, 1ssb,1a5p, 1a5q, 1c9v, 1c9x, 3rsp, 4rsd- bRNase I pancreatic (mutant)

3lxo, 3jw1, 3djo, 3djp, 3djq, 3djv, 3djx, 3dxg, 3dxh, 2w5g, 2w5i, 2w5k, 2w5l, 2w5m, 3d6o, 3d6p, 3d6q, 3d7b, 3d8y, 3d8z, 2qca, 2g8r, 1z6d, 1z6s, 1u1b, 1w4o, 1w4p, 1w4q, 1wbu, 1o0f, 1jn4, 1jvu, 1f0v, 1ruv, 1rnm, 1rnn, 1rbw, 1rca, 1rpf, 1rpg, 1rph, 1rbw, 1rca, 1rpf, 1rpg, 1rph, 1rnc, 1rnd, 1rob, 1rta, 1rtb,1afk, 1afl, 1eos, 1eow, 1o0h, 1o0m, 1o0n, 1o0o, 1qhc, 1rcn- bRNase I pancreatic + nucleotide

6rsa - bRNase I pancreatic + nucleotide - neutron

3fl0, 3fl1, 4rsk - bRNase I pancreatic (mutant) + nucleotide 2xog, 2xoi, 2q4g, 1dfj - bRNase I pancreatic + inhibitor

1rar, 1ras - bRNase I pancreatic fluorescent 2p42, 2p43, 2p44, 2p45, 2p46, 2p47, 2p48, 2p49, 2p4a, 1bzq - bRNase I + antibody

3f8g, 2e0j, 2e0l, 2e0m, 2e0o, 1h8x, 1e21, 1dza - hRNase I pancreatic (mutant) - human

2k11 - hRNase I pancreatic - NMR 1z7x - hRNase I + inhibitor

3ljd, 3ln8, 2vq8, 2vq9 - ZeRNase I – Zebrafish

2pqx, 2pqy - EcRNase I  - Escherichia coli

2z70, 2ea1 - EcRNAse I + DNA

===   RNase II===

2ix0, 2id0 - EcRNase II

2ix1 - EcRNase II (mutant)

1m58, 1km8, 1km9- BuRNase 2 - Bullfrog 1bc4 - BuRNase 2 - NMR 1m07 - BuRNase 2 + DNA 2bex - hRNase 2 + RNase inhibitor protein

2bzz, 2c01, 2c02, 2c05 - hRNase 2 + inhibitor

RNase III
2nue, 2nuf, 2nug, 1yyk, 1yyw - AaRNase III + RNA - Aquifex aeolicus

2ez6, 1yyo, 1yz9, 1rc7 - AaRNase III (mutant) + RNA

1rc5, 1i4s, 1jfz - AaRNase III N-terminal

1z5f - BuRNase III

2a11 - MtRNase III - Mycobacterium tuberculosis

1o0w - TmRNase III - Thermotoga maritima 1t4n, 1t4o - yRNase III – yeast - NMR 2kb5 - hRNase 3 - NMR 1dyt, 1qmt - hRNase 3

1h1h - hRNase 3 + nucleotide 2khx – hRNase III

3n3w, 2o2r - RNase III nuclease domain – Campylobacter jejuni

RNase 4
1wdy - hRNase 4

2rnf, 1rnf - hRNase 4 + nucleotide 1kvz - BuRNase 4 - NMR

RNase 5
1un3, 1un4, 1un5, 1gv7 - hRNase 5 (mutant)

1h0d - hRNase 5 + antibody

3lje - ZeRNase 5

RNase 6
1oj1, 1oj8 – BuRNase + nucleotide

RNase 7
2hky - hRNase 7 - NMR

RNase A
1rra - RNase A (mutant) – rat

RNase B
1rbb – bRNase B

1rbj - bRNase B + tetranucleotide

RNase BA
1x1u, 1x1x, 1x1y, 1b27, 1b2u, 1b3s, 1x1w - BaRNase BA + Barstar (mutant) - ''Bacillus amyloliquefaciens ''

3da7, 1brs, 1bgs - BaRNase BA + Barstar 1b2s, 2za4 - BaRNase BA (mutant) + Barstar (mutant)

1brn, 2kf5, 2kf6, 1rnb - BaRNase BA + nucleotide

3kch, 2f4y, 2f56, 2f5m, 2f5w - BaRNase BA crosslinked

2kf3, 2kf4, 1fw7, 1bnr - BaRNase BA – NMR 1yvs, 1b2x, 1a2p, 1bni, 1bnj - BaRNase BA

1b20, 1b21, 1b2z, 1bne, 1bnf, 1bng, 1brh, 1bri, 1brj, 1brk, 1bns, 1brg, 1bsa, 1bsb, 1bsc, 1bsd, 1bse, 1ban, 1bao - BaRNase BA (mutant)

RNase D
1yt3 - EcRNase D

RNase E
2vmk, 2c4r, 2bx2 - EcRNase E catalytic domain

1slj - EcRNase E S1 domain - NMR 1smx, 1sn8 - EcRNase E S1 domain

2vrt, 2c0b - EcRNase E catalytic domain + RNA

RNase F1
1fus, 1fut – GfRNase F1 + nucleotide – Gibberella fujikuroi

1rck, 1rcl - GfRNase F1 - NMR

RNase H
3h7i, 3h8s, 3h8w - T4RNase H (mutant) - Enterobacteria phage T4

2ihn - T4RNase H (mutant) + DNA 3h8j, 1tfr- T4RNase H 2rpi, 1ril - TtRNase H - Thermus thermophilus - NMR 1rbr, 1rbs, 1rbt, 1rbu, 1rbv, 2rn2 - EcRNase H

1lav, 1law, 1rda, 1rdb, 1rdc - EcRNase H (mutant) 1jl2 - EcRNase H /TtRNase H 3d0p - BhRNase H (mutant) + DNA - Bacillus halodurans

1zbf - BhRNase H (mutant) 2r7y, 2g8f, 2g8h, 2g8i, 2g8k, 2g8u, 2g8v, 2g8w, 1zbi, 1zbl - BhRNase H (mutant) + RNA + DNA 3ey1, 3i8d - BhRNase H (mutant) + D

RNase HI
2qk9, 2qkb, 2qkk - hRNase HI (mutant) + RNA + DNA 3h08 - RNase HI - Chlorobaculum tepidum

3aa2, 3aa3, 3aa4, 3aa5, 2yv0, 2z1g, 2z1h, 2z1i, 2z1j, 1wse, 1wsf, 1wsg, 1wsh, 1wsi, 1wsj, 1jxb, 1jl1, 1f21, 1kva, 1kvb, 1kvc, 1goa, 1gob, 1goc - EcRNase HI (mutant) 1g15, 1rdd, 1rnh - EcRNase HI

1rch - EcRNase HI - NMR 2zqb - SoRNase HI (mutant) - Shewanella oneidensis

2e4l - SoRNase HI 3bsu - hRNase HI catalytic domain + RNA + DNA 2ehg - RNase HI - Sulfolobus tokodaii 1qhk - yRNase HI N-terminal – NMR<BR />

RNase HII
3p83 - AfRNase HII + DNA polymerase sliding clamp - Archaeoglobus fulgidus

1i39, 1i3a - AfRNAse HII

3puf, 3p56, 3p5j - hRNAse H2 subunits α+β+γ

3kio - mRNase H2 subunits α+β+γ  - mouse

3o3g - TmRNase HII + DNA<BR /> 3o3f, 3o3h - TmRNase HII (mutant) + DNA<BR /> 2etj - TmRNase HII

1x1p, 1io2 - TkRNase HII

2dfe, 2dff, 2dfh - TkRNase HII (mutant) - ''Thermococcus kodakarensis ''

1eke - RNase HII - ''Methanocalcococcus jannaschii  ''

2d0a, 2d0b, 2d0c - RNase HIII - Geobacillus stearothermophilus

1uax - PhRNase HIII – Pyrococcus horikoshii

RNase J
3bk1 - TtRNase J

3bk2 - TtRNase J + nucleotide

RNase LE
1dix - RNase LE - Solanum lycopersicum

RNase MAR1
1xn4 - RNase MAR1 – Leishmania major

2b34 - RNase MAR1 – Caenorhabditis elegans

RNase MS
1rms, 1rds - RNase MS + nucleotide - Aspergillus phoenicis

RNase MC1
1v9h, 1j1f, 1j1g - McRNase MC1 (mutant) + nucleotide - Momordica charantia

1ucg - McRNase MC1 (mutant)

1ucd, 1uca, 1ucc  - McRNase MC1 + nucleotide

1bk7 - McRNase MC1

RNase NT
1vcz, 1vd1, 1vd3 - NgRNase NT + nucleotide] - Nicotiana glutinosa

1iyb - NgRNase NW

RNase P
3ok7, 3okb, 3q1q, 3q1r - TmRNase P + TmRNase P RNA + tRNA Phe

1nz0 - TmRNase P

1d6t - RNase P - Staphylococcus aureus

2a64 - RNase P (mutant) - ''Bacillus stearothermophilus  ''

1a6f, 1nbs - BsRNase P (mutant) - Bacillus subtilis

1ts9, 1tsf – AfRNase P

1u9s – RNase P – synthetic

2avs - PfRNase P (mutant) – Pyrococcus furiosus

2k3r, 2ki7 - PfRNase P

2cvz, 2zae – PhRNase P

RNase PH
3dd6 - RNase PH - ''Bacillus anthracis ''

1oyp, 1oyr, 1oys - BsRNase PH

1r6l, 1r6m - PaRNase PH - ''Pseudomonas aeruginosa ''

3b4t - MtRNase PH - Mycobacterium tuberculosis

1udn - AaRNase PH

1udo, 1udq, 1uds - AaRNase PH (mutant)

RNase RH
1bol – Rhizopus niveus

RNase S
3oqy, 3oqz, 3or0, 1z3l, 1z3m, 1z3p, 1y92, 1y94, 1fev, 1d5d, 1d5e, 1d5h, 2rln, 1qwq - bRNase S seminal (mutant)

1tq9, 1r5c, 11ba, 11bg - bRNase S + nucleotide 1r5d, 1r3m, 1n1x, 1n3z, 1j7z, 1j80, 1j81, 1j82, 1cjq, 1cjr, 1bsr,1rbc, 1rbd, 1rbe, 1rbf, 1rbg, 1rbh, 1rbi, 1rnu, 1rnv, 2rns - bRNase S

1b6v - bRNase S/bRNase A

RNase S3
1iqq - RNase S3 - Japanese pear

RNase SA
3a5e, 1zgx, 1ynv, 1t2h, 1t2i, 1uci, 1ucj, 1uck, 1ucl, 1i70, 1i8v, 1box - SaRNase SA guanyl-specific (mutant) - ''Streptomyces aureofaciens ''

1lni,1c54, 1rge, 1rgf, 1rgg, 1rgh, 1sar - SaRNase SA

1gmp, 1gmq, 1gmr, 2sar - SaRNase SA +nucleotide 1ay7 - SaRNase SA + Barstar

1rsn - SaRNase SA + cyclophosphothiolate

RNase SA2
1py3, 1pyl - SaRNase SA2

3dgy, 3dh2, 3d4a, 3d5g, 3d5i - SaRNase SA2 + mononucleotide

RNase SA3
1mgr, 1mgw - SaRNase SA3

RNase SF11
1ioo - RNase SF11 - Nicotiana alata

RNase T
2is3 - EcRNase T

2f96 - PaRNase T

3ngy – EcRNase T (mutant) + His tag

3ngz - EcRNase T (mutant) + nucleotide

3nh0, 3nh1, 3nh2 - EcRNase T + nucleotide

RNase T1
1tto,1rn1, 1rn4, 1rnt, 2aad, 2aae - AoRNase T1 - Aspergillus oryzae

1q9e, 1iyy, 1i2e, 1i2f, 1i2g, 1i3f, 1i3i, 1hz1, 1fys, 1fzu, 1ch0, 4bir, 3bir, 5bir,1g02, 1hyf, 1trp, 1trq, 2bir, 4rnt, 5rnt, 6rnt, 7rnt, 8rnt, 9rnt - AoRNase T1 (mutant)

1lov, 1low, 1loy, 1i0v, 1i0x, 1b2m, 1rhl, 1bir, 1rgk, 1rgl - AoRNase T1 (mutant) + nucleotide

1bvi, 2bu4, 2hoh, 4hoh, 5hoh, 3hoh, 2gsp, 3gsp, 4gsp, 5gsp, 6gsp, 7gsp, 1gsp, 1det, 1rls, 1lra, 1rga,1bu4, 1rgc, 2rnt, 3bu4, 4bu4, 5bu4 - AoRNase T1 + nucleotide 3rnt - AoRNase T1 + V

1ygw - AoRNase T1 – NMR<BR />

RNase U2
3agn, 3ago, 3ahw - UsRNase U2 + AMP - ''Ustilago sphaerogena ''

1rtu - UsRNase U2

RNase U2B
3ahs - UsRNase U2B

RNase Z
2e7y - TmRNase Z

2fk6 - BsRNase Z (mutant) + tRNA Thr 1y44 - BsRNase Z (mutant)

2cbn – EcRNase Z

RNase α-sarcin
1de3 - αsRNase – Aspergillus giganteus

1r4y - αsRNase (mutant)

Oligoribonuclease
2igi, 1yta – EcORNase

2gbz - ORNase - Xanthomonas campestris

1j9a - ORNase - Haemophilus influenzae

Polynucleotide Phosphorylase
3cdi - EcPNPase

3gll - EcPNPase core

3cdj - EcPNPase C-terminal truncated

1e3h, 1e3p - PNPase - Streptomyces antibioticus

3gcm, 3gme, 3h1c - EcPNPase + RNase E recognition domain

3h36 - PNPase fragment - Streptococcus mutans

Binase
1gou, 1gov, 1goy – BiBinase – Bacillus intermedius

2rbi – BiBinase (mutant)

Poly(A)-specific RNase
1ug8 – mParn R3H domain - NMR<BR /> 1whv – mParn RNA-binding domain - NMR<BR /> 2rok - mParn CAP-binding domain - NMR<BR /> 3d45 - mParn + nucleotide

2a1s - hParn

2a1r, 3ctr – hParn + nucleotide

2zpo – RNase – Chelonia mydas

3a4y, 3idz, 3ie0, 3ie2 – TtRNase (mutant) – Thermus thermophilus

3iek - TtRNase

3ie1, 3iem - TtRNase (mutant) + RNA

3iel - TtRNase + nucleotide